4CMN

Crystal structure of OCRL in complex with a phosphate ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases.

Tresaugues, L.Silvander, C.Flodin, S.Welin, M.Nyman, T.Graslund, S.Hammarstrom, M.Berglund, H.Nordlund, P.

(2014) Structure 22: 744

  • DOI: 10.1016/j.str.2014.01.013
  • Primary Citation of Related Structures:  
    3MTC, 3N9V, 3NR8, 4CMN, 4CML

  • PubMed Abstract: 
  • SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phop ...

    SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.


    Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, 637551, Singapore. Electronic address: par.nordlund@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1A354Homo sapiensMutation(s): 1 
Gene Names: OCRLOCRL1
EC: 3.1.3.36 (PDB Primary Data), 3.1.3.56 (UniProt), 3.1.3.86 (UniProt)
Find proteins for Q01968 (Homo sapiens)
Explore Q01968 
Go to UniProtKB:  Q01968
NIH Common Fund Data Resources
PHAROS  Q01968
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.215 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.766α = 90
b = 146.766β = 90
c = 146.766γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references